Index (jmztabm-api 1.0.6 API)

A B C D E F G H I L M N O P Q R S T U V W
All Classes All Packages

A

ABUNDANCE_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant ABUNDANCE_PREFIX="abundance_"
abundanceAssay - de.isas.mztab2.model.SmallMoleculeFeature.Properties
abundanceAssay - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for abundanceAssay.
abundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceAssay.
AbundanceColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant AbundanceColumn
AbundanceColumnSameId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AbundanceColumnSameId
AbundanceColumnTogether - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AbundanceColumnTogether
abundanceStudyVariable - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceStudyVariable.
abundanceVariationStudyVariable - de.isas.mztab2.model.SmallMoleculeSummary.Properties
abundanceVariationStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for abundanceVariationStudyVariable.
accession - de.isas.mztab2.model.PublicationItem.Properties
accession(String) - Method in class de.isas.mztab2.model.PublicationItem: Builder method for accession.
add(MZTabError) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: A limit max capacity list, if contains a couple of MZTabError objects.
addAbundanceAssayItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single abundanceAssayItem to the abundanceAssay collection.
addAbundanceAssayItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceAssayItem to the abundanceAssay collection.
addAbundanceStudyVariableItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceStudyVariableItem to the abundanceStudyVariable collection.
addAbundanceVariationStudyVariableItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single abundanceVariationStudyVariableItem to the abundanceVariationStudyVariable collection.
addAdductIonsItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single adductIonsItem to the adductIons collection.
addAll(List<MZTabError>) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: A limit max capacity list, if contains a couple of MZTabError objects.
addAnalyzerItem(Parameter) - Method in class de.isas.mztab2.model.Instrument: Add a single analyzerItem to the analyzer collection.
addAssayItem(Assay) - Method in class de.isas.mztab2.model.Metadata: Add a single assayItem to the assay collection.
addAssayRefsItem(Assay) - Method in class de.isas.mztab2.model.StudyVariable: Add a single assayRefsItem to the assayRefs collection.
addCellTypeItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single cellTypeItem to the cellType collection.
addChemicalFormulaItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single chemicalFormulaItem to the chemicalFormula collection.
addChemicalNameItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single chemicalNameItem to the chemicalName collection.
addColunitSmallMoleculeEvidenceItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeEvidenceItem to the colunitSmallMoleculeEvidence collection.
addColunitSmallMoleculeFeatureItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeFeatureItem to the colunitSmallMoleculeFeature collection.
addColunitSmallMoleculeItem(ColumnParameterMapping) - Method in class de.isas.mztab2.model.Metadata: Add a single colunitSmallMoleculeItem to the colunitSmallMolecule collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.MzTab: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single commentItem to the comment collection.
addCommentItem(Comment) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single commentItem to the comment collection.
addContactItem(Contact) - Method in class de.isas.mztab2.model.Metadata: Add a single contactItem to the contact collection.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Assay: Add a single customItem to the custom collection.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single customItem to the custom collection.
addCustomItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single customItem to the custom collection.
addCvItem(CV) - Method in class de.isas.mztab2.model.Metadata: Add a single cvItem to the cv collection.
addDatabaseIdentifierItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single databaseIdentifierItem to the databaseIdentifier collection.
addDatabaseItem(Database) - Method in class de.isas.mztab2.model.Metadata: Add a single databaseItem to the database collection.
addDerivatizationAgentItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single derivatizationAgentItem to the derivatizationAgent collection.
addDiseaseItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single diseaseItem to the disease collection.
addExternalStudyUriItem(Uri) - Method in class de.isas.mztab2.model.Metadata: Add a single externalStudyUriItem to the externalStudyUri collection.
addFactorsItem(Parameter) - Method in class de.isas.mztab2.model.StudyVariable: Add a single factorsItem to the factors collection.
addFragmentationMethodItem(Parameter) - Method in class de.isas.mztab2.model.MsRun: Add a single fragmentationMethodItem to the fragmentationMethod collection.
addIdConfidenceMeasureItem(Parameter) - Method in class de.isas.mztab2.model.Metadata: Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
addIdConfidenceMeasureItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single idConfidenceMeasureItem to the idConfidenceMeasure collection.
addInchiItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single inchiItem to the inchi collection.
addInstrumentItem(Instrument) - Method in class de.isas.mztab2.model.Metadata: Add a single instrumentItem to the instrument collection.
addMsRunItem(MsRun) - Method in class de.isas.mztab2.model.Metadata: Add a single msRunItem to the msRun collection.
addMsRunRefItem(MsRun) - Method in class de.isas.mztab2.model.Assay: Add a single msRunRefItem to the msRunRef collection.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single optItem to the opt collection.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single optItem to the opt collection.
addOptItem(OptColumnMapping) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single optItem to the opt collection.
addPublicationItem(Publication) - Method in class de.isas.mztab2.model.Metadata: Add a single publicationItem to the publication collection.
addPublicationItemsItem(PublicationItem) - Method in class de.isas.mztab2.model.Publication: Add a single publicationItemsItem to the publicationItems collection.
addSampleItem(Sample) - Method in class de.isas.mztab2.model.Metadata: Add a single sampleItem to the sample collection.
addSampleProcessingItem(Parameter) - Method in class de.isas.mztab2.model.SampleProcessing: Add a single sampleProcessingItem to the sampleProcessing collection.
addSampleProcessingItem(SampleProcessing) - Method in class de.isas.mztab2.model.Metadata: Add a single sampleProcessingItem to the sampleProcessing collection.
addScanPolarityItem(Parameter) - Method in class de.isas.mztab2.model.MsRun: Add a single scanPolarityItem to the scanPolarity collection.
addSettingItem(String) - Method in class de.isas.mztab2.model.Software: Add a single settingItem to the setting collection.
addSmallMoleculeEvidenceItem(SmallMoleculeEvidence) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeEvidenceItem to the smallMoleculeEvidence collection.
addSmallMoleculeFeatureItem(SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeFeatureItem to the smallMoleculeFeature collection.
addSmallMoleculeSummaryItem(SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTab: Add a single smallMoleculeSummaryItem to the smallMoleculeSummary collection.
addSmeIdRefsItem(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Add a single smeIdRefsItem to the smeIdRefs collection.
addSmfIdRefsItem(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single smfIdRefsItem to the smfIdRefs collection.
addSmilesItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single smilesItem to the smiles collection.
addSoftwareItem(Software) - Method in class de.isas.mztab2.model.Metadata: Add a single softwareItem to the software collection.
addSpeciesItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single speciesItem to the species collection.
addSpectraRefItem(SpectraRef) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Add a single spectraRefItem to the spectraRef collection.
addStudyVariableItem(StudyVariable) - Method in class de.isas.mztab2.model.Metadata: Add a single studyVariableItem to the studyVariable collection.
addTheoreticalNeutralMassItem(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single theoreticalNeutralMassItem to the theoreticalNeutralMass collection.
addTissueItem(Parameter) - Method in class de.isas.mztab2.model.Sample: Add a single tissueItem to the tissue collection.
adductIon - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
adductIon - de.isas.mztab2.model.SmallMoleculeFeature.Properties
adductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for adductIon.
adductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for adductIon.
adductIons - de.isas.mztab2.model.SmallMoleculeSummary.Properties
adductIons(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for adductIons.
addUriItem(Uri) - Method in class de.isas.mztab2.model.Metadata: Add a single uriItem to the uri collection.
addUriItem(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Add a single uriItem to the uri collection.
affiliation - de.isas.mztab2.model.Contact.Properties
affiliation(String) - Method in class de.isas.mztab2.model.Contact: Builder method for affiliation.
AmbiguityMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AmbiguityMod
analyzer - de.isas.mztab2.model.Instrument.Properties
analyzer(List<Parameter>) - Method in class de.isas.mztab2.model.Instrument: Builder method for analyzer.
assay - de.isas.mztab2.model.Metadata.Properties
assay(List<Assay>) - Method in class de.isas.mztab2.model.Metadata: Builder method for assay.
Assay - Class in de.isas.mztab2.model: Specification of assay.
Assay() - Constructor for class de.isas.mztab2.model.Assay
Assay.Properties - Enum in de.isas.mztab2.model: Property enumeration for Assay.
AssayNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AssayNotDefined
assayRefs - de.isas.mztab2.model.StudyVariable.Properties
assayRefs(List<Assay>) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for assayRefs.
AssayRefs - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant AssayRefs
averageFunction - de.isas.mztab2.model.StudyVariable.Properties
averageFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for averageFunction.

B

BAR - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant BAR='|'
BAR_S - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant BAR='|'
bestIdConfidenceMeasure - de.isas.mztab2.model.SmallMoleculeSummary.Properties
bestIdConfidenceMeasure(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for bestIdConfidenceMeasure.
bestIdConfidenceValue - de.isas.mztab2.model.SmallMoleculeSummary.Properties
bestIdConfidenceValue(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for bestIdConfidenceValue.

C

CALCULATE_ERROR - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant CALCULATE_ERROR="NaN"
category - de.isas.mztab2.model.ValidationMessage.Properties
category(ValidationMessage.CategoryEnum) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for category.
cellType - de.isas.mztab2.model.Sample.Properties
cellType(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for cellType.
charge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
charge - de.isas.mztab2.model.SmallMoleculeFeature.Properties
charge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for charge.
charge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for charge.
CheckParameter - Annotation Type in de.isas.lipidomics.mztab2.validation.constraints: JAVAX validation compliant annotation.
chemicalFormula - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
chemicalFormula - de.isas.mztab2.model.SmallMoleculeSummary.Properties
chemicalFormula(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for chemicalFormula.
chemicalFormula(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for chemicalFormula.
chemicalName - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
chemicalName - de.isas.mztab2.model.SmallMoleculeSummary.Properties
chemicalName(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for chemicalName.
chemicalName(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for chemicalName.
CHEMMODS - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant CHEMMODS
CHEMMODSAccession - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant CHEMMODSAccession
clear() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Clear all errors stored in the error list.
code - de.isas.mztab2.model.Error.Properties
code - de.isas.mztab2.model.ValidationMessage.Properties
code(Integer) - Method in class de.isas.mztab2.model.Error: Builder method for code.
code(String) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for code.
COLON - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant COLON=':'
columnName - de.isas.mztab2.model.ColumnParameterMapping.Properties
columnName(String) - Method in class de.isas.mztab2.model.ColumnParameterMapping: Builder method for columnName.
ColumnNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ColumnNotValid
ColumnParameterMapping - Class in de.isas.mztab2.model: Defines the used unit for a column in the mzTab-M file.
ColumnParameterMapping() - Constructor for class de.isas.mztab2.model.ColumnParameterMapping
ColumnParameterMapping.Properties - Enum in de.isas.mztab2.model: Property enumeration for ColumnParameterMapping.
ColUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant ColUnit
colunitSmallMolecule - de.isas.mztab2.model.Metadata.Properties
colunitSmallMolecule(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMolecule.
colunitSmallMoleculeEvidence - de.isas.mztab2.model.Metadata.Properties
colunitSmallMoleculeEvidence(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMoleculeEvidence.
colunitSmallMoleculeFeature - de.isas.mztab2.model.Metadata.Properties
colunitSmallMoleculeFeature(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata: Builder method for colunitSmallMoleculeFeature.
COM - de.isas.mztab2.model.Comment.PrefixEnum
COMMA - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant COMMA=','
comment - de.isas.mztab2.model.MzTab.Properties
comment - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
comment - de.isas.mztab2.model.SmallMoleculeFeature.Properties
comment - de.isas.mztab2.model.SmallMoleculeSummary.Properties
comment(List<Comment>) - Method in class de.isas.mztab2.model.MzTab: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for comment.
comment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for comment.
Comment - Class in de.isas.mztab2.model: Comment lines can be placed anywhere in an mzTab file.
Comment() - Constructor for class de.isas.mztab2.model.Comment
Comment.PrefixEnum - Enum in de.isas.mztab2.model: Gets or Sets prefix
Comment.Properties - Enum in de.isas.mztab2.model: Property enumeration for Comment.
contact - de.isas.mztab2.model.Metadata.Properties
contact(List<Contact>) - Method in class de.isas.mztab2.model.Metadata: Builder method for contact.
Contact - Class in de.isas.mztab2.model: The contact’s name, affiliation and e-mail.
Contact() - Constructor for class de.isas.mztab2.model.Contact
Contact.Properties - Enum in de.isas.mztab2.model: Property enumeration for Contact.
convertToValidationMessages() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Converts this error list to a list of validation messages.
convertToValidationMessages(MZTabErrorList) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Converts the provided error list to a list of validation messages.
CountMatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant CountMatch
createError(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Error by parse keyword.
createInfo(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Info by parse keyword.
createWarn(MZTabErrorType.Category, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Generate a MZTabErrorType.Level.Warn by parse keyword.
CROSS_CHECK - de.isas.mztab2.model.ValidationMessage.CategoryEnum
CrossCheck - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
CrossCheckErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Provide crosscheck service, that is parse the consistent between current mztab file and some other resource (eg, database, xml file and so on).
custom - de.isas.mztab2.model.Assay.Properties
custom - de.isas.mztab2.model.Metadata.Properties
custom - de.isas.mztab2.model.Sample.Properties
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Assay: Builder method for custom.
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for custom.
custom(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for custom.
cv - de.isas.mztab2.model.Metadata.Properties
cv(List<CV>) - Method in class de.isas.mztab2.model.Metadata: Builder method for cv.
CV - Class in de.isas.mztab2.model: Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
CV() - Constructor for class de.isas.mztab2.model.CV
CV_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant CV_PREFIX="cv_"
CV.Properties - Enum in de.isas.mztab2.model: Property enumeration for CV.
cvAccession - de.isas.mztab2.model.Parameter.Properties
cvAccession(String) - Method in class de.isas.mztab2.model.Parameter: Builder method for cvAccession.
cvLabel - de.isas.mztab2.model.Parameter.Properties
cvLabel(String) - Method in class de.isas.mztab2.model.Parameter: Builder method for cvLabel.
CvTermMalformed - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermMalformed
CvTermNotAllowed - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermNotAllowed
CvTermNotInRule - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermNotInRule
CvTermOptional - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermOptional
CvTermRecommended - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermRecommended
CvTermRequired - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermRequired
CvTermXor - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvTermXor
CvUndefinedInMetadata - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvUndefinedInMetadata
CvUnused - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType: Constant CvUnused

D

database - de.isas.mztab2.model.Metadata.Properties
database(List<Database>) - Method in class de.isas.mztab2.model.Metadata: Builder method for database.
Database - Class in de.isas.mztab2.model: Specification of databases.
Database() - Constructor for class de.isas.mztab2.model.Database
Database.Properties - Enum in de.isas.mztab2.model: Property enumeration for Database.
databaseIdentifier - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
databaseIdentifier - de.isas.mztab2.model.SmallMoleculeSummary.Properties
databaseIdentifier(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for databaseIdentifier.
databaseIdentifier(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for databaseIdentifier.
de.isas.lipidomics.mztab2.validation - package de.isas.lipidomics.mztab2.validation: This package contains classes that provide the basic validator infrastructure used in the jmztabm-validation module.
de.isas.lipidomics.mztab2.validation.constraints - package de.isas.lipidomics.mztab2.validation.constraints: This package contains custom validation annotations for the javax.validation framework.
de.isas.lipidomics.mztab2.validation.validators - package de.isas.lipidomics.mztab2.validation.validators: This package contains custom validators that implement the
de.isas.mztab2.model - package de.isas.mztab2.model: Base package for the jmztab-m data model, generated from the mzTab_m_swagger.yml specification.
derivatizationAgent - de.isas.mztab2.model.Metadata.Properties
derivatizationAgent(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for derivatizationAgent.
derivatizedForm - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
derivatizedForm(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for derivatizedForm.
description - de.isas.mztab2.model.Metadata.Properties
description - de.isas.mztab2.model.Sample.Properties
description - de.isas.mztab2.model.StudyVariable.Properties
description(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for description.
description(String) - Method in class de.isas.mztab2.model.Sample: Builder method for description.
description(String) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for description.
detector - de.isas.mztab2.model.Instrument.Properties
detector(Parameter) - Method in class de.isas.mztab2.model.Instrument: Builder method for detector.
disease - de.isas.mztab2.model.Sample.Properties
disease(List<Parameter>) - Method in class de.isas.mztab2.model.Sample: Builder method for disease.
DOI - de.isas.mztab2.model.PublicationItem.TypeEnum
Double - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Double
DoubleList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant DoubleList
DuplicationAccession - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationAccession
DuplicationDefine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationDefine
DuplicationID - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant DuplicationID

E

email - de.isas.mztab2.model.Contact.Properties
email(String) - Method in class de.isas.mztab2.model.Contact: Builder method for email.
Email - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Email
ENCODE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant ENCODE="getProperty(mztab.encode)"
equals(Object) - Method in class de.isas.mztab2.model.Assay
equals(Object) - Method in class de.isas.mztab2.model.ColumnParameterMapping
equals(Object) - Method in class de.isas.mztab2.model.Comment
equals(Object) - Method in class de.isas.mztab2.model.Contact
equals(Object) - Method in class de.isas.mztab2.model.CV
equals(Object) - Method in class de.isas.mztab2.model.Database
equals(Object) - Method in class de.isas.mztab2.model.Error
equals(Object) - Method in class de.isas.mztab2.model.IndexedElementImpl
equals(Object) - Method in class de.isas.mztab2.model.Instrument
equals(Object) - Method in class de.isas.mztab2.model.Metadata
equals(Object) - Method in class de.isas.mztab2.model.MsRun
equals(Object) - Method in class de.isas.mztab2.model.MzTab
equals(Object) - Method in class de.isas.mztab2.model.OptColumnMapping
equals(Object) - Method in class de.isas.mztab2.model.Parameter
equals(Object) - Method in class de.isas.mztab2.model.Publication
equals(Object) - Method in class de.isas.mztab2.model.PublicationItem
equals(Object) - Method in class de.isas.mztab2.model.Sample
equals(Object) - Method in class de.isas.mztab2.model.SampleProcessing
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeFeature
equals(Object) - Method in class de.isas.mztab2.model.SmallMoleculeSummary
equals(Object) - Method in class de.isas.mztab2.model.Software
equals(Object) - Method in class de.isas.mztab2.model.SpectraRef
equals(Object) - Method in class de.isas.mztab2.model.StringList
equals(Object) - Method in class de.isas.mztab2.model.StudyVariable
equals(Object) - Method in class de.isas.mztab2.model.Uri
equals(Object) - Method in class de.isas.mztab2.model.ValidationMessage
equals(Object) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
Error - Class in de.isas.mztab2.model: Error
Error - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
Error() - Constructor for class de.isas.mztab2.model.Error
ERROR - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
ERROR_AMBIGUITY - Static variable in exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constant ERROR_AMBIGUITY="mzTab do not support one protein in mor"{trunked}
Error.Properties - Enum in de.isas.mztab2.model: Property enumeration for Error.
evidenceInputId - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
evidenceInputId(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for evidenceInputId.
expMassToCharge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
expMassToCharge - de.isas.mztab2.model.SmallMoleculeFeature.Properties
expMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for expMassToCharge.
expMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for expMassToCharge.
ExternalStudyFormatNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ExternalStudyFormatNotDefined
ExternalStudyIdFormatNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ExternalStudyIdFormatNotDefined
externalStudyUri - de.isas.mztab2.model.Metadata.Properties
externalStudyUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata: Builder method for externalStudyUri.
externalUri - de.isas.mztab2.model.Assay.Properties
externalUri(String) - Method in class de.isas.mztab2.model.Assay: Builder method for externalUri.

F

factors - de.isas.mztab2.model.StudyVariable.Properties
factors(List<Parameter>) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for factors.
findLevel(String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: findLevel.
FixedMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant FixedMod
forLevel(MZTabErrorType.Category, MZTabErrorType.Level, String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
format - de.isas.mztab2.model.MsRun.Properties
format(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for format.
Format - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
FORMAT - de.isas.mztab2.model.ValidationMessage.CategoryEnum
FormatErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Diagnose different types of format-related (reporting format problems).
fragmentationMethod - de.isas.mztab2.model.MsRun.Properties
fragmentationMethod(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun: Builder method for fragmentationMethod.
fromValue(String) - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
fromValue(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
fullName - de.isas.mztab2.model.CV.Properties
fullName(String) - Method in class de.isas.mztab2.model.CV: Builder method for fullName.

G

getAbundanceAssay() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The feature’s abundance in every assay described in the metadata section MUST be reported.
getAbundanceAssay() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s abundance in every assay described in the metadata section MUST be reported.
getAbundanceFor(Assay, SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided assay and small molecule feature object.
getAbundanceFor(Assay, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided assay and small molecule summary object.
getAbundanceFor(StudyVariable, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance value for the provided study variable and small molecule summary object.
getAbundanceStudyVariable() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays).
getAbundanceVariationFor(StudyVariable, SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieves the abundance variation value for the provided study variable and small molecule summary object.
getAbundanceVariationStudyVariable() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable.
getAccession() - Method in class de.isas.mztab2.model.PublicationItem: The native accession id for this publication item.
getAdductIon() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAdductIon() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAdductIons() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A “|” separated list of detected adducts for this this molecule, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g.
getAffiliation() - Method in class de.isas.mztab2.model.Contact: The contact's affiliation.
getAnalyzer() - Method in class de.isas.mztab2.model.Instrument: The instrument's mass analyzer, as defined by the parameter.
getAssay() - Method in class de.isas.mztab2.model.Metadata: Specification of assay.
getAssayFor(OptColumnMapping, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the assay referenced by id from the columnMapping identifier.
getAssayFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the assay referenced by id from the metadata section.
getAssayRefs() - Method in class de.isas.mztab2.model.StudyVariable: The assays referenced by this study variable.
getAverageFunction() - Method in class de.isas.mztab2.model.StudyVariable: The function used to calculate summarised small molecule quantities over the assays referenced by this study variable.
getBestIdConfidenceMeasure() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The approach or database search that identified this small molecule with highest confidence.
getBestIdConfidenceValue() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The best confidence measure in identification (for this type of score) for the given small molecule across all assays.
getCategory() - Method in class de.isas.mztab2.model.ValidationMessage: Get category.
getCategory() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field category.
getCause() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field cause.
getCellType() - Method in class de.isas.mztab2.model.Sample: Biological cell type information on the sample.
getCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence’s charge value using positive integers both for positive and negative polarity modes.
getCharge() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The feature’s charge value using positive integers both for positive and negative polarity modes.
getChemicalFormula() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons).
getChemicalFormula() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential chemical formulae of the reported compound.
getChemicalName() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule’s chemical/common name, or general description if a chemical name is unavailable.
getChemicalName() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable.
getCode() - Method in class de.isas.mztab2.model.Error: Get code.
getCode() - Method in class de.isas.mztab2.model.ValidationMessage: Get code.
getCode() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field code.
getColumnName() - Method in class de.isas.mztab2.model.ColumnParameterMapping: The fully qualified target column name.
getColunitSmallMolecule() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule section.
getColunitSmallMoleculeEvidence() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule evidence section.
getColunitSmallMoleculeFeature() - Method in class de.isas.mztab2.model.Metadata: Defines the used unit for a column in the small molecule feature section.
getComment() - Method in class de.isas.mztab2.model.MzTab: Comment lines can be placed anywhere in an mzTab file.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Get comment.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Get comment.
getComment() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Get comment.
getContact() - Method in class de.isas.mztab2.model.Metadata: The contact’s name, affiliation and e-mail.
getCustom() - Method in class de.isas.mztab2.model.Assay: Additional user or cv parameters.
getCustom() - Method in class de.isas.mztab2.model.Metadata: Any additional parameters describing the analysis reported.
getCustom() - Method in class de.isas.mztab2.model.Sample: Additional user or cv parameters.
getCv() - Method in class de.isas.mztab2.model.Metadata: Specification of controlled vocabularies. label: A string describing the labels of the controlled vocabularies/ontologies used in the mzTab file as a short-hand e.g.
getCvAccession() - Method in class de.isas.mztab2.model.Parameter: Get cvAccession.
getCvLabel() - Method in class de.isas.mztab2.model.Parameter: Get cvLabel.
getDatabase() - Method in class de.isas.mztab2.model.Metadata: Specification of databases.
getDatabaseFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the database referenced by id from the metadata section.
getDatabaseIdentifier() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The putative identification for the small molecule sourced from an external database, using the same prefix specified in database[1-n]-prefix.
getDatabaseIdentifier() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule.
getDerivatizationAgent() - Method in class de.isas.mztab2.model.Metadata: A description of derivatization agents applied to small molecules, using userParams or CV terms where possible.
getDerivatizedForm() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: If a derivatized form has been analysed by MS, then the functional group attached to the molecule should be reported here using suitable userParam or CV terms as appropriate.
getDescription() - Method in class de.isas.mztab2.model.Metadata: The file’s human readable description.
getDescription() - Method in class de.isas.mztab2.model.Sample: A free form description of the sample.
getDescription() - Method in class de.isas.mztab2.model.StudyVariable: A free-form description of this study variable.
getDetector() - Method in class de.isas.mztab2.model.Instrument: The instrument's detector, as defined by the parameter.
getDisease() - Method in class de.isas.mztab2.model.Sample: Disease information on the sample.
getElementType() - Method in class de.isas.mztab2.model.IndexedElementImpl: Returns the element type string.
getEmail() - Method in class de.isas.mztab2.model.Contact: The contact's e-mail address.
getError() - Method in exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Getter for the field error.
getError(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Returns the element at the specified position in this list.
getErrorList() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Unmodifiable list of errors
getEvidenceInputId() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair, isotope profile that was used for the identification process, to serve as a grouping mechanism, whereby multiple rows of results from the same input data share the same ID.
getEvidences(SmallMoleculeFeature) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule evidences in order of definition for the provided small molecule feature.
getEvidencesByEvidenceInputId(String) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule evidences for the provided evidence input id.
getExpMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The experimental mass/charge value for the precursor ion.
getExpMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value.
getExternalStudyUri() - Method in class de.isas.mztab2.model.Metadata: A URI pointing to an external file with more details about the study design (e.g., an ISA-TAB file).
getExternalUri() - Method in class de.isas.mztab2.model.Assay: An external URI to further information about this assay.
getFactors() - Method in class de.isas.mztab2.model.StudyVariable: Parameters indicating which factors were used for the assays referenced by this study variable, and at which levels.
getFeatures(SmallMoleculeSummary) - Method in class de.isas.mztab2.model.MzTabAccess: Retrieve all small molecule features in order of definition for the provided small molecule summary.
getFormat() - Method in class de.isas.mztab2.model.MsRun: The msRun's file format.
getFragmentationMethod() - Method in class de.isas.mztab2.model.MsRun: The fragmentation methods applied during this msRun.
getFullName() - Method in class de.isas.mztab2.model.CV: The full name of this CV, for humans.
getHash() - Method in class de.isas.mztab2.model.MsRun: The file hash value of this msRun's data file.
getHashMethod() - Method in class de.isas.mztab2.model.MsRun: The hash method used to calculate the file hash.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence table header prefix.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The small molecule feature table header prefix.
getHeaderPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule table header prefix.
getId() - Method in class de.isas.mztab2.model.Assay: Get id.
getId() - Method in class de.isas.mztab2.model.Contact: Get id.
getId() - Method in class de.isas.mztab2.model.CV: Get id.
getId() - Method in class de.isas.mztab2.model.Database: Get id.
getId() - Method in interface de.isas.mztab2.model.IndexedElement: Returns the id of the indexed element.
getId() - Method in class de.isas.mztab2.model.IndexedElementImpl
getId() - Method in class de.isas.mztab2.model.Instrument: Get id.
getId() - Method in class de.isas.mztab2.model.MsRun: Get id.
getId() - Method in class de.isas.mztab2.model.Parameter: Get id.
getId() - Method in class de.isas.mztab2.model.Publication: Get id.
getId() - Method in class de.isas.mztab2.model.Sample: Get id.
getId() - Method in class de.isas.mztab2.model.SampleProcessing: Get id.
getId() - Method in class de.isas.mztab2.model.Software: Get id.
getId() - Method in class de.isas.mztab2.model.StudyVariable: Get id.
getId() - Method in class de.isas.mztab2.model.Uri: Get id.
getIdConfidenceMeasure() - Method in class de.isas.mztab2.model.Metadata: The type of small molecule confidence measures or scores MUST be reported as a CV parameter [1-n].
getIdConfidenceMeasure() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Any statistical value or score for the identification.
getIdentificationMethod() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The database search, search engine or process that was used to identify this small molecule e.g. the name of software, database or manual curation etc.
getIdentifier() - Method in class de.isas.mztab2.model.OptColumnMapping: The fully qualified column name.
getIdFormat() - Method in class de.isas.mztab2.model.MsRun: The msRun's mass spectra id format.
getInchi() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A standard IUPAC International Chemical Identifier (InChI) for the given substance.
getInchi() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance.
getInstrument() - Method in class de.isas.mztab2.model.Metadata: The name, source, analyzer and detector of the instruments used in the experiment.
getInstrumentRef() - Method in class de.isas.mztab2.model.MsRun: The instrument on which this msRun was measured.
getIsotopomer() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null.
getLabel() - Method in class de.isas.mztab2.model.CV: The abbreviated CV label.
getLevel() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Getter for the field level.
getLevel() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field level.
getLineNumber() - Method in class de.isas.mztab2.model.Comment: Get lineNumber.
getLineNumber() - Method in class de.isas.mztab2.model.ValidationMessage: Get lineNumber.
getLineNumber() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field lineNumber.
getLocation() - Method in class de.isas.mztab2.model.MsRun: The msRun's location URI.
getMaxErrorCount() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Getter for the field maxErrorCount.
getMessage() - Method in class de.isas.mztab2.model.Error: Get message.
getMessage() - Method in class de.isas.mztab2.model.ValidationMessage: Get message.
getMessage() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field message.
getMessageType() - Method in class de.isas.mztab2.model.ValidationMessage: Get messageType.
getMetadata() - Method in class de.isas.mztab2.model.MzTab: Get metadata.
getMsg() - Method in class de.isas.mztab2.model.Comment: Get msg.
getMsLevel() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The highest MS level used to inform identification e.g.
getMsRun() - Method in class de.isas.mztab2.model.Metadata: Specification of ms_run.
getMsRun() - Method in class de.isas.mztab2.model.SpectraRef: The ms run object reference by this spectral reference.
getMsRunFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the ms run referenced by id from the metadata section.
getMsRunRef() - Method in class de.isas.mztab2.model.Assay: The ms run(s) referenced by this assay.
getMzTabID() - Method in class de.isas.mztab2.model.Metadata: The ID of the mzTab file, this could be supplied by the repository from which it is downloaded or a local identifier from the lab producing the file.
getMzTabVersion() - Method in class de.isas.mztab2.model.Metadata: The version of the mzTab file.
getName() - Method in class de.isas.mztab2.model.Assay: The assay name.
getName() - Method in class de.isas.mztab2.model.Contact: The contact's name.
getName() - Method in class de.isas.mztab2.model.Instrument: Get name.
getName() - Method in class de.isas.mztab2.model.MsRun: The msRun's name.
getName() - Method in class de.isas.mztab2.model.Parameter: Get name.
getName() - Method in class de.isas.mztab2.model.Sample: The sample's name.
getName() - Method in class de.isas.mztab2.model.StudyVariable: The study variable name.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Additional columns can be added to the end of the small molecule evidence table.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Additional columns can be added to the end of the small molecule feature table.
getOpt() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Additional columns can be added to the end of the small molecule table.
getOriginal() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Getter for the field original.
getParam() - Method in class de.isas.mztab2.model.ColumnParameterMapping: The parameter specifying the unit.
getParam() - Method in class de.isas.mztab2.model.Database: The parameter to identify this database.
getParam() - Method in class de.isas.mztab2.model.OptColumnMapping: The (optional) parameter for this column.
getParameter() - Method in class de.isas.mztab2.model.Software: Parameter defining the software being used.
getPayload() - Method in class de.isas.mztab2.model.IndexedElementImpl: Returns the wrapped object.
getPrefix() - Method in class de.isas.mztab2.model.Comment: Get prefix.
getPrefix() - Method in class de.isas.mztab2.model.Database: The database prefix.
getPrefix() - Method in class de.isas.mztab2.model.Metadata: The metadata section prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The small molecule evidence table row prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The small molecule feature table row prefix.
getPrefix() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule table row prefix.
getProperty(String) - Static method in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: getProperty.
getPropertyName() - Method in enum de.isas.mztab2.model.Assay.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Comment.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Contact.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.CV.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Database.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Error.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Instrument.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Metadata.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.MsRun.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.MzTab.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Parameter.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Publication.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Sample.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Software.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.Uri.Properties
getPropertyName() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
getPublication() - Method in class de.isas.mztab2.model.Metadata: A publication associated with this file.
getPublicationItems() - Method in class de.isas.mztab2.model.Publication: The publication item ids referenced by this publication.
getQuantificationMethod() - Method in class de.isas.mztab2.model.Metadata: The quantification method used in the experiment reported in the file.
getRank() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The rank of this identification from this approach as increasing integers from 1 (best ranked identification).
getReference() - Method in class de.isas.mztab2.model.SpectraRef: The (vendor-dependendent) reference string to the actual mass spectrum.
getReliability() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The reliability of the given small molecule identification.
getRetentionTimeInSeconds() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The apex of the feature on the retention time axis, in a Master or aggregate MS run.
getRetentionTimeInSecondsEnd() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The end time of the feature on the retention time axis, in a Master or aggregate MS run.
getRetentionTimeInSecondsStart() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: The start time of the feature on the retention time axis, in a Master or aggregate MS run.
getSample() - Method in class de.isas.mztab2.model.Metadata: Specification of sample.
getSampleProcessing() - Method in class de.isas.mztab2.model.Metadata: A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.
getSampleProcessing() - Method in class de.isas.mztab2.model.SampleProcessing: Parameters specifiying sample processing that was applied within one step.
getSampleRef() - Method in class de.isas.mztab2.model.Assay: The sample referenced by this assay.
getScanPolarity() - Method in class de.isas.mztab2.model.MsRun: The scan polarity/polarities used during this msRun.
getSetting() - Method in class de.isas.mztab2.model.Software: A software setting used.
getSmallMoleculeEvidence() - Method in class de.isas.mztab2.model.MzTab: The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.
getSmallMoleculeFeature() - Method in class de.isas.mztab2.model.MzTab: The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.
getSmallMoleculeFeatureQuantificationUnit() - Method in class de.isas.mztab2.model.Metadata: Defines what type of units are reported in the small molecule feature quantification / abundance fields.
getSmallMoleculeIdentificationReliability() - Method in class de.isas.mztab2.model.Metadata: The system used for giving reliability / confidence codes to small molecule identifications MUST be specified if not using the default codes.
getSmallMoleculeQuantificationUnit() - Method in class de.isas.mztab2.model.Metadata: Defines what type of units are reported in the small molecule summary quantification / abundance fields.
getSmallMoleculeSummary() - Method in class de.isas.mztab2.model.MzTab: The small molecule section is table-based.
getSmeId() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A within file unique identifier for the small molecule evidence result.
getSmeIdRefAmbiguityCode() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams.
getSmeIdRefs() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: References to the identification evidence (SME elements) via referencing SME_ID values.
getSmfId() - Method in class de.isas.mztab2.model.SmallMoleculeFeature: A within file unique identifier for the small molecule feature.
getSmfIdRefs() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values.
getSmiles() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.
getSmiles() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A list of “|” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule.
getSmlId() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A within file unique identifier for the small molecule.
getSoftware() - Method in class de.isas.mztab2.model.Metadata: Software used to analyze the data and obtain the reported results.
getSource() - Method in class de.isas.mztab2.model.Instrument: The instrument's source, as defined by the parameter.
getSpecies() - Method in class de.isas.mztab2.model.Sample: Biological species information on the sample.
getSpectraRef() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.
getStudyVariable() - Method in class de.isas.mztab2.model.Metadata: Specification of study_variable.
getStudyVariableFor(Integer, Metadata) - Method in class de.isas.mztab2.model.MzTabAccess: Tries to locate the study variable referenced by id from the metadata section.
getTheoreticalMassToCharge() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: The theoretical mass/charge value for the small molecule or the database mass/charge value (for a spectral library match).
getTheoreticalNeutralMass() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: The small molecule’s precursor’s theoretical neutral mass.
getTissue() - Method in class de.isas.mztab2.model.Sample: Biological tissue information on the sample.
getTitle() - Method in class de.isas.mztab2.model.Metadata: The file’s human readable title.
getType() - Method in class de.isas.mztab2.model.PublicationItem: The type qualifier of this publication item.
getType() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: Getter for the field type.
getType(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: getType.
getTypeMap() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: Getter for the field typeMap.
getUri() - Method in class de.isas.mztab2.model.CV: A URI to the CV definition.
getUri() - Method in class de.isas.mztab2.model.Database: The URI to the online database.
getUri() - Method in class de.isas.mztab2.model.Metadata: A URI pointing to the file’s source data (e.g., a MetaboLights records).
getUri() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).
getUri() - Method in class de.isas.mztab2.model.SmallMoleculeSummary: A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry).
getValue() - Method in enum de.isas.mztab2.model.Comment.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.Metadata.PrefixEnum
getValue() - Method in class de.isas.mztab2.model.OptColumnMapping: The value for this column in a particular row.
getValue() - Method in class de.isas.mztab2.model.Parameter: Get value.
getValue() - Method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
getValue() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
getValue() - Method in class de.isas.mztab2.model.Uri: The URI pointing to the external resource.
getValue() - Method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
getValue() - Method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType
getValues() - Static method in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType
getVariationFunction() - Method in class de.isas.mztab2.model.StudyVariable: The function used to calculate the variation of small molecule quantities over the assays referenced by this study variable.
getVersion() - Method in class de.isas.mztab2.model.CV: The CV version used when the file was generated.
getVersion() - Method in class de.isas.mztab2.model.Database: The database version.
GLOBAL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant GLOBAL="global"
GOTermList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant GOTermList
groups() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter

H

hash - de.isas.mztab2.model.MsRun.Properties
hash(String) - Method in class de.isas.mztab2.model.MsRun: Builder method for hash.
hashCode() - Method in class de.isas.mztab2.model.Assay
hashCode() - Method in class de.isas.mztab2.model.ColumnParameterMapping
hashCode() - Method in class de.isas.mztab2.model.Comment
hashCode() - Method in class de.isas.mztab2.model.Contact
hashCode() - Method in class de.isas.mztab2.model.CV
hashCode() - Method in class de.isas.mztab2.model.Database
hashCode() - Method in class de.isas.mztab2.model.Error
hashCode() - Method in class de.isas.mztab2.model.IndexedElementImpl
hashCode() - Method in class de.isas.mztab2.model.Instrument
hashCode() - Method in class de.isas.mztab2.model.Metadata
hashCode() - Method in class de.isas.mztab2.model.MsRun
hashCode() - Method in class de.isas.mztab2.model.MzTab
hashCode() - Method in class de.isas.mztab2.model.OptColumnMapping
hashCode() - Method in class de.isas.mztab2.model.Parameter
hashCode() - Method in class de.isas.mztab2.model.Publication
hashCode() - Method in class de.isas.mztab2.model.PublicationItem
hashCode() - Method in class de.isas.mztab2.model.Sample
hashCode() - Method in class de.isas.mztab2.model.SampleProcessing
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeFeature
hashCode() - Method in class de.isas.mztab2.model.SmallMoleculeSummary
hashCode() - Method in class de.isas.mztab2.model.Software
hashCode() - Method in class de.isas.mztab2.model.SpectraRef
hashCode() - Method in class de.isas.mztab2.model.StringList
hashCode() - Method in class de.isas.mztab2.model.StudyVariable
hashCode() - Method in class de.isas.mztab2.model.Uri
hashCode() - Method in class de.isas.mztab2.model.ValidationMessage
hashCode() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType
hashMethod - de.isas.mztab2.model.MsRun.Properties
hashMethod(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for hashMethod.
HeaderLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant HeaderLine
HeaderNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant HeaderNotValid
headerPrefix - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
headerPrefix - de.isas.mztab2.model.SmallMoleculeFeature.Properties
headerPrefix - de.isas.mztab2.model.SmallMoleculeSummary.Properties

I

id - de.isas.mztab2.model.Assay.Properties
id - de.isas.mztab2.model.Contact.Properties
id - de.isas.mztab2.model.CV.Properties
id - de.isas.mztab2.model.Database.Properties
id - de.isas.mztab2.model.Instrument.Properties
id - de.isas.mztab2.model.MsRun.Properties
id - de.isas.mztab2.model.Parameter.Properties
id - de.isas.mztab2.model.Publication.Properties
id - de.isas.mztab2.model.Sample.Properties
id - de.isas.mztab2.model.SampleProcessing.Properties
id - de.isas.mztab2.model.Software.Properties
id - de.isas.mztab2.model.StudyVariable.Properties
id - de.isas.mztab2.model.Uri.Properties
id(Integer) - Method in class de.isas.mztab2.model.Assay: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Contact: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.CV: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Database: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Instrument: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.MsRun: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Parameter: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Publication: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Sample: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.SampleProcessing: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Software: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.StudyVariable: Builder method for id.
id(Integer) - Method in class de.isas.mztab2.model.Uri: Builder method for id.
idConfidenceMeasure - de.isas.mztab2.model.Metadata.Properties
idConfidenceMeasure - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
idConfidenceMeasure(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata: Builder method for idConfidenceMeasure.
idConfidenceMeasure(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for idConfidenceMeasure.
identificationMethod - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
identificationMethod(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for identificationMethod.
identifier - de.isas.mztab2.model.OptColumnMapping.Properties
identifier(String) - Method in class de.isas.mztab2.model.OptColumnMapping: Builder method for identifier.
idFormat - de.isas.mztab2.model.MsRun.Properties
idFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun: Builder method for idFormat.
IdNumber - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant IdNumber
inchi - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
inchi - de.isas.mztab2.model.SmallMoleculeSummary.Properties
inchi(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for inchi.
inchi(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary: Builder method for inchi.
IndexedElement - Interface in de.isas.mztab2.model: Indexed elements (IDs) define a unique ID for a collection of multiple metadata elements of the same type within the mzTab-M document, e.g. for sample, assay, study variable etc.
IndexedElement - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant IndexedElement
IndexedElementImpl - Class in de.isas.mztab2.model: Implementation of IndexedElement where more information is required than just the id.
IndexedElementImpl(Integer, String, Object) - Constructor for class de.isas.mztab2.model.IndexedElementImpl: Create a new indexed element implementation for the provided id, element type and payload.
INFINITY - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant INFINITY="INF"
Info - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
INFO - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
instrument - de.isas.mztab2.model.Metadata.Properties
instrument(List<Instrument>) - Method in class de.isas.mztab2.model.Metadata: Builder method for instrument.
Instrument - Class in de.isas.mztab2.model: The name, source, analyzer and detector of the instruments used in the experiment.
Instrument() - Constructor for class de.isas.mztab2.model.Instrument
Instrument.Properties - Enum in de.isas.mztab2.model: Property enumeration for Instrument.
instrumentRef - de.isas.mztab2.model.MsRun.Properties
instrumentRef(Instrument) - Method in class de.isas.mztab2.model.MsRun: Builder method for instrumentRef.
Integer - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant Integer
IntegerList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant IntegerList
InvalidColunitFormat - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant InvalidColunitFormat
isEmpty() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Returns true if this list contains no elements.
isEmpty(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils: Check the string is null or blank.
isotopomer - de.isas.mztab2.model.SmallMoleculeFeature.Properties
isotopomer(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeFeature: Builder method for isotopomer.
isValid(Parameter, ConstraintValidatorContext) - Method in interface de.isas.lipidomics.mztab2.validation.validators.ParameterValidator
ItemNumberMismatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ItemNumberMismatch

L

label - de.isas.mztab2.model.CV.Properties
label(String) - Method in class de.isas.mztab2.model.CV: Builder method for label.
LEVEL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant LEVEL
lineNumber - de.isas.mztab2.model.Comment.Properties
lineNumber - de.isas.mztab2.model.ValidationMessage.Properties
lineNumber(Integer) - Method in class de.isas.mztab2.model.Comment: Builder method for lineNumber.
lineNumber(Long) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for lineNumber.
LineOrder - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant LineOrder
LinePrefix - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant LinePrefix
location - de.isas.mztab2.model.MsRun.Properties
location(String) - Method in class de.isas.mztab2.model.MsRun: Builder method for location.
Logical - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category
LOGICAL - de.isas.mztab2.model.ValidationMessage.CategoryEnum
LogicalErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: Reporting errors related to the logical relationships among the different sections in a file.

M

MAX_ERROR_COUNT - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MAX_ERROR_COUNT=Integer.parseInt(getProperty("mztab.max_error_count"))
message - de.isas.mztab2.model.Error.Properties
message - de.isas.mztab2.model.ValidationMessage.Properties
message() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
message(String) - Method in class de.isas.mztab2.model.Error: Builder method for message.
message(String) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for message.
messageCode() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
messageType - de.isas.mztab2.model.ValidationMessage.Properties
messageType(ValidationMessage.MessageTypeEnum) - Method in class de.isas.mztab2.model.ValidationMessage: Builder method for messageType.
metadata - de.isas.mztab2.model.MzTab.Properties
metadata(Metadata) - Method in class de.isas.mztab2.model.MzTab: Builder method for metadata.
Metadata - Class in de.isas.mztab2.model: The metadata section provides additional information about the dataset(s) reported in the mzTab file.
Metadata() - Constructor for class de.isas.mztab2.model.Metadata
Metadata.PrefixEnum - Enum in de.isas.mztab2.model: The metadata section prefix.
Metadata.Properties - Enum in de.isas.mztab2.model: Property enumeration for Metadata.
MINUS - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants: Constant MINUS='-'
ModificationList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant ModificationList
ModificationPosition - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant ModificationPosition
msg - de.isas.mztab2.model.Comment.Properties
msg(String) - Method in class de.isas.mztab2.model.Comment: Builder method for msg.
msLevel - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
msLevel(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence: Builder method for msLevel.
msRun - de.isas.mztab2.model.Metadata.Properties
msRun - de.isas.mztab2.model.SpectraRef.Properties
msRun(MsRun) - Method in class de.isas.mztab2.model.SpectraRef: Builder method for msRun.
msRun(List<MsRun>) - Method in class de.isas.mztab2.model.Metadata: Builder method for msRun.
MsRun - Class in de.isas.mztab2.model: Specification of ms_run.
MsRun() - Constructor for class de.isas.mztab2.model.MsRun
MsRun.Properties - Enum in de.isas.mztab2.model: Property enumeration for MsRun.
MsRunHashMethodNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunHashMethodNotDefined
MsRunLocation - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunLocation
MsRunNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType: Constant MsRunNotDefined
MsRunOptionalColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MsRunOptionalColumn
msRunRef - de.isas.mztab2.model.Assay.Properties
msRunRef(List<MsRun>) - Method in class de.isas.mztab2.model.Assay: Builder method for msRunRef.
MTD - de.isas.mztab2.model.Metadata.PrefixEnum
MTDDefineLabel - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MTDDefineLabel
MTDLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MTDLine
MZBoolean - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZBoolean
MzTab - Class in de.isas.mztab2.model: mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches.
MzTab() - Constructor for class de.isas.mztab2.model.MzTab
MZTAB_ERROR_OVERFLOW_EXCEPTION_MESSAGE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MZTAB_ERROR_OVERFLOW_EXCEPTION_MESSAGE="System error queue overflow!
MZTAB_EXCEPTION_MESSAGE - Static variable in class uk.ac.ebi.pride.jmztab2.utils.MZTabProperties: Constant MZTAB_EXCEPTION_MESSAGE="There exist errors in the metadata sect"{trunked}
MzTab.Properties - Enum in de.isas.mztab2.model: Property enumeration for MzTab.
MzTabAccess - Class in de.isas.mztab2.model: Utility class for easier access to linked information within an mztab-M data object.
MzTabAccess(MzTab) - Constructor for class de.isas.mztab2.model.MzTabAccess: Create an MzTabAccess object for the provided mzTab object.
MZTabConstants - Class in uk.ac.ebi.pride.jmztab2.model: Define a couple of constants used in the jmzTab API.
MZTabConstants() - Constructor for class uk.ac.ebi.pride.jmztab2.model.MZTabConstants
MZTabConversionException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: Runtime exception for mzTab conversion
MZTabConversionException() - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(String) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(String, Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabConversionException(Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabConversionException: Constructor for MZTabConversionException.
MZTabError - Class in uk.ac.ebi.pride.jmztab2.utils.errors: mzTab files can be validated to ensure that they comply with the latest version of the format specification.
MZTabError(MZTabErrorType, int, String...) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError: System will fill a couple of values one by one, and generate a concrete error message during parse MZTabError.lineNumber line in mzTab file.
MZTabErrorList - Class in uk.ac.ebi.pride.jmztab2.utils.errors: A limit max capacity list, if contains a couple of MZTabError objects.
MZTabErrorList() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, which max size is MZTabProperties.MAX_ERROR_COUNT, and only allow MZTabErrorType.Level.Error or greater level errors to be added into list.
MZTabErrorList(MZTabErrorType.Level) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, which max size is MZTabProperties.MAX_ERROR_COUNT
MZTabErrorList(MZTabErrorType.Level, int) - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList: Generate a error list, with given error level and maximum error count.
MZTabErrorOverflowException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: If error count great than MZTabProperties.MAX_ERROR_COUNT System will stop validate and throw overflow exception.
MZTabErrorOverflowException() - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorOverflowException: If error count great than MZTabProperties.MAX_ERROR_COUNT System will stop validate and throw overflow exception.
MZTabErrorType - Class in uk.ac.ebi.pride.jmztab2.utils.errors: MZTabErrorType class.
MZTabErrorType() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType: Constructor for MZTabErrorType.
MZTabErrorType.Category - Enum in uk.ac.ebi.pride.jmztab2.utils.errors
MZTabErrorType.Level - Enum in uk.ac.ebi.pride.jmztab2.utils.errors: We classify diagnosis message types into three levels: Info, Warn and Error, all of them coming from the notational conventions of the specification.
MZTabErrorTypeMap - Class in uk.ac.ebi.pride.jmztab2.utils.errors: This list class used to storage all types of MZTabError, and provide query service based on the error/warn code.
MZTabErrorTypeMap() - Constructor for class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorTypeMap: Constructor for MZTabErrorTypeMap.
MZTabException - Exception in uk.ac.ebi.pride.jmztab2.utils.errors: Wrap a MZTabError.
MZTabException(String) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
MZTabException(MZTabError) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
MZTabException(MZTabError, Throwable) - Constructor for exception uk.ac.ebi.pride.jmztab2.utils.errors.MZTabException: Constructor for MZTabException.
mzTabID - de.isas.mztab2.model.Metadata.Properties
mzTabID(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for mzTabID.
MZTabId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabType
MZTabMode - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabMode
MZTabProperties - Class in uk.ac.ebi.pride.jmztab2.utils: This class will load the properties used by the mzTab-M library for message formatting during validation.
MZTabStringUtils - Class in uk.ac.ebi.pride.jmztab2.model: Provide a couple of functions for translate, parse and print formatted string defined in the mzTab specification.
MZTabType - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabType
MzTabValidator - Class in de.isas.lipidomics.mztab2.validation: Delegating validator implementation that forwards validation to the provided validator implementations.
MzTabValidator(Validator<MzTab>...) - Constructor for class de.isas.lipidomics.mztab2.validation.MzTabValidator
mzTabVersion - de.isas.mztab2.model.Metadata.Properties
mzTabVersion(String) - Method in class de.isas.mztab2.model.Metadata: Builder method for mzTabVersion.
MZTabVersion - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType: Constant MZTabVersion





N

name - de.isas.mztab2.model.Assay.Properties
 
name - de.isas.mztab2.model.Contact.Properties
 
name - de.isas.mztab2.model.Instrument.Properties
 
name - de.isas.mztab2.model.MsRun.Properties
 
name - de.isas.mztab2.model.Parameter.Properties
 
name - de.isas.mztab2.model.Sample.Properties
 
name - de.isas.mztab2.model.StudyVariable.Properties
 
name(Parameter) - Method in class de.isas.mztab2.model.Instrument

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Assay

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Contact

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.MsRun

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Parameter

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.Sample

Builder method for name.

name(String) - Method in class de.isas.mztab2.model.StudyVariable

Builder method for name.

NEW_LINE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant NEW_LINE="System.getProperty(line.separator)"

NoDatabaseMustHaveNullPrefix - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoDatabaseMustHaveNullPrefix

NoHeaderLine - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoHeaderLine

NoMetadataSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoMetadataSection

NoSmallMoleculeEvidenceSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeEvidenceSection

NoSmallMoleculeFeatureQuantificationUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeFeatureQuantificationUnit

NoSmallMoleculeFeatureSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeFeatureSection

NoSmallMoleculeIdentificationReliability - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeIdentificationReliability

NoSmallMoleculeQuantificationUnit - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeQuantificationUnit

NoSmallMoleculeSummarySection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NoSmallMoleculeSummarySection

NotDefineInHeader - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotDefineInHeader

NotDefineInMetadata - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotDefineInMetadata

NotNULL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NotNULL

NULL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant NULL="null"

NULL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant NULL





O

of(Object) - Static method in interface de.isas.mztab2.model.IndexedElement

Create a new indexed element as a proxy of the provided element.

of(String) - Static method in enum de.isas.mztab2.model.Assay.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Comment.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Contact.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.CV.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Database.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Error.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Instrument.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Metadata.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.MsRun.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.MzTab.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Parameter.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Publication.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.PublicationItem.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Sample.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Software.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.SpectraRef.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.StudyVariable.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.Uri.Properties
 
of(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
opt - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
opt - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
opt - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for opt.

opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for opt.

opt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for opt.

OPT_PREFIX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant OPT_PREFIX="opt_"

OptColumnMapping - Class in de.isas.mztab2.model

Additional columns can be added to the end of the small molecule table.

OptColumnMapping() - Constructor for class de.isas.mztab2.model.OptColumnMapping
 
OptColumnMapping.Properties - Enum in de.isas.mztab2.model

Property enumeration for OptColumnMapping.

OptionalCVParamColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant OptionalCVParamColumn





P

param - de.isas.mztab2.model.ColumnParameterMapping.Properties
 
param - de.isas.mztab2.model.Database.Properties
 
param - de.isas.mztab2.model.OptColumnMapping.Properties
 
param(Parameter) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Builder method for param.

param(Parameter) - Method in class de.isas.mztab2.model.Database

Builder method for param.

param(Parameter) - Method in class de.isas.mztab2.model.OptColumnMapping

Builder method for param.

Param - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Param

ParamAccessionNotNamespaced - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant ParamAccessionNotNamespaced

parameter - de.isas.mztab2.model.Software.Properties
 
parameter(Parameter) - Method in class de.isas.mztab2.model.Software

Builder method for parameter.

Parameter - Class in de.isas.mztab2.model

mzTab makes use of CV parameters.

Parameter() - Constructor for class de.isas.mztab2.model.Parameter
 
Parameter.Properties - Enum in de.isas.mztab2.model

Property enumeration for Parameter.

ParameterValidator - Interface in de.isas.lipidomics.mztab2.validation.validators

Base interface for parameter validation with default validation method.

ParamList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant ParamList

parseString(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils

Pre-process the String object.

payload() - Method in annotation type de.isas.lipidomics.mztab2.validation.constraints.CheckParameter
 
PeptideSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PeptideSearchEngineScoreNotDefined

PeptideSection - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PeptideSection

prefix - de.isas.mztab2.model.Comment.Properties
 
prefix - de.isas.mztab2.model.Database.Properties
 
prefix - de.isas.mztab2.model.Metadata.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
prefix - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
prefix(Comment.PrefixEnum) - Method in class de.isas.mztab2.model.Comment

Builder method for prefix.

prefix(Metadata.PrefixEnum) - Method in class de.isas.mztab2.model.Metadata

Builder method for prefix.

prefix(String) - Method in class de.isas.mztab2.model.Database

Builder method for prefix.

print(OutputStream) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Print error list to output stream.

ProteinCoverage - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant ProteinCoverage

ProteinSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant ProteinSearchEngineScoreNotDefined

PSMSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant PSMSearchEngineScoreNotDefined

publication - de.isas.mztab2.model.Metadata.Properties
 
publication(List<Publication>) - Method in class de.isas.mztab2.model.Metadata

Builder method for publication.

Publication - Class in de.isas.mztab2.model

A publication associated with this file.

Publication - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Publication

Publication() - Constructor for class de.isas.mztab2.model.Publication
 
Publication.Properties - Enum in de.isas.mztab2.model

Property enumeration for Publication.

PublicationItem - Class in de.isas.mztab2.model

A publication item, defined by a qualifier and a native accession, e.g. pubmed id.

PublicationItem() - Constructor for class de.isas.mztab2.model.PublicationItem
 
PublicationItem.Properties - Enum in de.isas.mztab2.model

Property enumeration for PublicationItem.

PublicationItem.TypeEnum - Enum in de.isas.mztab2.model

The type qualifier of this publication item.

publicationItems - de.isas.mztab2.model.Publication.Properties
 
publicationItems(List<PublicationItem>) - Method in class de.isas.mztab2.model.Publication

Builder method for publicationItems.

PUBMED - de.isas.mztab2.model.PublicationItem.TypeEnum
 




Q

QuantificationAbundance - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant QuantificationAbundance

quantificationMethod - de.isas.mztab2.model.Metadata.Properties
 
quantificationMethod(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for quantificationMethod.





R

rank - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
rank(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for rank.

reference - de.isas.mztab2.model.SpectraRef.Properties
 
reference(String) - Method in class de.isas.mztab2.model.SpectraRef

Builder method for reference.

REGEX_ABUNDANCE_ASSAY_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ABUNDANCE_ASSAY_COLUMN_NAME="assay\\[(\\d+)\\]"

REGEX_ABUNDANCE_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ABUNDANCE_COLUMN_NAME="abundance_(.+)"

REGEX_ADDUCT - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_ADDUCT="^\[\d*M([+-][\w\d]+)*\]\d*[+-]$"

REGEX_CV_PARAM_OPT_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_CV_PARAM_OPT_COLUMN_NAME="cv(_([A-Za-z0-9\\-\\[\\]:\\.]+))?


REGEX_DEFAULT_RELIABILITY - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_DEFAULT_RELIABILITY="[1234]{1}"

REGEX_EMAIL - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_EMAIL="[_A-Za-z0-9-]+(\\.


REGEX_INDEXED_VALUE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_INDEXED_VALUE="\\[(\\d+)\\]"

REGEX_MZTAB_M - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_MZTAB_M="(?<major>[2]{1})\\.(?<minor>\\d{1})\\.(?<micro>\\d{1})-(?<profile>[M]{1})"

REGEX_NORMAL_METADATA - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_NORMAL_METADATA="(\\w+)(\\[(\\w+)\\])?


REGEX_OPT_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_OPT_COLUMN_NAME="opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)"

REGEX_PARAM_SPLIT - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_PARAM_SPLIT=",(?


REGEX_SPECTRA_REF_FILE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_FILE = "file=[\\w]+"

REGEX_SPECTRA_REF_INDEX - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_INDEX = "index=[\\d]+"

REGEX_SPECTRA_REF_MZML_UNIQUE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_MZML_UNIQUE = "[\\w]+"

REGEX_SPECTRA_REF_SCAN - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_SCAN = "scan=[\\d]+"

REGEX_SPECTRA_REF_SPECTRUM - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_SPECTRUM = "spectrum=[\\d]+"

REGEX_SPECTRA_REF_THERMO_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_THERMO_NATIVE = "controllerType=[\\d]+ controllerNumber=[1-9]\\d* scan=[1-9]\\d*"

REGEX_SPECTRA_REF_WATERS_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_WATERS_NATIVE = "function=[1-9]\\d* process=[\\d]+ scan=[\\d]+"

REGEX_SPECTRA_REF_WIFF_NATIVE - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_SPECTRA_REF_WIFF_NATIVE = "sample=[\\d]+ period=[\\d]+ cycle=[\\d]+ experiment=[\\d]+"

REGEX_STUDY_VARIABLE_COLUMN_NAME - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant REGEX_STUDY_VARIABLE_COLUMN_NAME="study_variable\\[(\\d+)\\]"

RegexMismatch - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant RegexMismatch

reliability - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
reliability(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for reliability.

Reliability - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Reliability

retentionTimeInSeconds - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSeconds(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSeconds.

retentionTimeInSecondsEnd - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSecondsEnd(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSecondsEnd.

retentionTimeInSecondsStart - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
retentionTimeInSecondsStart(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for retentionTimeInSecondsStart.

RulePointerObjectNullOptional - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullOptional

RulePointerObjectNullRecommended - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullRecommended

RulePointerObjectNullRequired - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant RulePointerObjectNullRequired





S

sample - de.isas.mztab2.model.Metadata.Properties
 
sample(List<Sample>) - Method in class de.isas.mztab2.model.Metadata

Builder method for sample.

Sample - Class in de.isas.mztab2.model

Specification of sample.

Sample() - Constructor for class de.isas.mztab2.model.Sample
 
Sample.Properties - Enum in de.isas.mztab2.model

Property enumeration for Sample.

sampleProcessing - de.isas.mztab2.model.Metadata.Properties
 
sampleProcessing - de.isas.mztab2.model.SampleProcessing.Properties
 
sampleProcessing(List<Parameter>) - Method in class de.isas.mztab2.model.SampleProcessing

Builder method for sampleProcessing.

sampleProcessing(List<SampleProcessing>) - Method in class de.isas.mztab2.model.Metadata

Builder method for sampleProcessing.

SampleProcessing - Class in de.isas.mztab2.model

A list of parameters describing a sample processing, preparation or handling step similar to a biological or analytical methods report.

SampleProcessing() - Constructor for class de.isas.mztab2.model.SampleProcessing
 
SampleProcessing.Properties - Enum in de.isas.mztab2.model

Property enumeration for SampleProcessing.

sampleRef - de.isas.mztab2.model.Assay.Properties
 
sampleRef(Sample) - Method in class de.isas.mztab2.model.Assay

Builder method for sampleRef.

scanPolarity - de.isas.mztab2.model.MsRun.Properties
 
scanPolarity(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Builder method for scanPolarity.

SearchEngineScore - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant SearchEngineScore

SEH - de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
 
SemanticValidationException - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant SemanticValidationException

Sequence - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant Sequence

setAbundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set abundanceAssay.

setAbundanceAssay(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceAssay.

setAbundanceStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceStudyVariable.

setAbundanceVariationStudyVariable(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set abundanceVariationStudyVariable.

setAccession(String) - Method in class de.isas.mztab2.model.PublicationItem

Set accession.

setAdductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set adductIon.

setAdductIon(String) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set adductIon.

setAdductIons(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set adductIons.

setAffiliation(String) - Method in class de.isas.mztab2.model.Contact

Set affiliation.

setAnalyzer(List<Parameter>) - Method in class de.isas.mztab2.model.Instrument

Set analyzer.

setAssay(List<Assay>) - Method in class de.isas.mztab2.model.Metadata

Set assay.

setAssayRefs(List<Assay>) - Method in class de.isas.mztab2.model.StudyVariable

Set assayRefs.

setAverageFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Set averageFunction.

setBestIdConfidenceMeasure(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set bestIdConfidenceMeasure.

setBestIdConfidenceValue(Double) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set bestIdConfidenceValue.

setCategory(ValidationMessage.CategoryEnum) - Method in class de.isas.mztab2.model.ValidationMessage

Set category.

setCellType(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set cellType.

setCharge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set charge.

setCharge(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set charge.

setChemicalFormula(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set chemicalFormula.

setChemicalFormula(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set chemicalFormula.

setChemicalName(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set chemicalName.

setChemicalName(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set chemicalName.

setCode(Integer) - Method in class de.isas.mztab2.model.Error

Set code.

setCode(String) - Method in class de.isas.mztab2.model.ValidationMessage

Set code.

setColumnName(String) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Set columnName.

setColunitSmallMolecule(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMolecule.

setColunitSmallMoleculeEvidence(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMoleculeEvidence.

setColunitSmallMoleculeFeature(List<ColumnParameterMapping>) - Method in class de.isas.mztab2.model.Metadata

Set colunitSmallMoleculeFeature.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.MzTab

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set comment.

setComment(List<Comment>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set comment.

setContact(List<Contact>) - Method in class de.isas.mztab2.model.Metadata

Set contact.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Assay

Set custom.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set custom.

setCustom(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set custom.

setCv(List<CV>) - Method in class de.isas.mztab2.model.Metadata

Set cv.

setCvAccession(String) - Method in class de.isas.mztab2.model.Parameter

Set cvAccession.

setCvLabel(String) - Method in class de.isas.mztab2.model.Parameter

Set cvLabel.

setDatabase(List<Database>) - Method in class de.isas.mztab2.model.Metadata

Set database.

setDatabaseIdentifier(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set databaseIdentifier.

setDatabaseIdentifier(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set databaseIdentifier.

setDerivatizationAgent(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set derivatizationAgent.

setDerivatizedForm(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set derivatizedForm.

setDescription(String) - Method in class de.isas.mztab2.model.Metadata

Set description.

setDescription(String) - Method in class de.isas.mztab2.model.Sample

Set description.

setDescription(String) - Method in class de.isas.mztab2.model.StudyVariable

Set description.

setDetector(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set detector.

setDisease(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set disease.

setEmail(String) - Method in class de.isas.mztab2.model.Contact

Set email.

setEvidenceInputId(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set evidenceInputId.

setExpMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set expMassToCharge.

setExpMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set expMassToCharge.

setExternalStudyUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Set externalStudyUri.

setExternalUri(String) - Method in class de.isas.mztab2.model.Assay

Set externalUri.

setFactors(List<Parameter>) - Method in class de.isas.mztab2.model.StudyVariable

Set factors.

setFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set format.

setFragmentationMethod(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Set fragmentationMethod.

setFullName(String) - Method in class de.isas.mztab2.model.CV

Set fullName.

setHash(String) - Method in class de.isas.mztab2.model.MsRun

Set hash.

setHashMethod(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set hashMethod.

setId(Integer) - Method in class de.isas.mztab2.model.Assay

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Contact

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.CV

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Database

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Instrument

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.MsRun

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Parameter

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Publication

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Sample

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.SampleProcessing

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Software

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.StudyVariable

Set id.

setId(Integer) - Method in class de.isas.mztab2.model.Uri

Set id.

setIdConfidenceMeasure(List<Parameter>) - Method in class de.isas.mztab2.model.Metadata

Set idConfidenceMeasure.

setIdConfidenceMeasure(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set idConfidenceMeasure.

setIdentificationMethod(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set identificationMethod.

setIdentifier(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Set identifier.

setIdFormat(Parameter) - Method in class de.isas.mztab2.model.MsRun

Set idFormat.

setInchi(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set inchi.

setInchi(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set inchi.

setInstrument(List<Instrument>) - Method in class de.isas.mztab2.model.Metadata

Set instrument.

setInstrumentRef(Instrument) - Method in class de.isas.mztab2.model.MsRun

Set instrumentRef.

setIsotopomer(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set isotopomer.

setLabel(String) - Method in class de.isas.mztab2.model.CV

Set label.

setLevel(MZTabErrorType.Level) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Define the level of the errors that are going to be store in the list.

setLineNumber(Integer) - Method in class de.isas.mztab2.model.Comment

Set lineNumber.

setLineNumber(Long) - Method in class de.isas.mztab2.model.ValidationMessage

Set lineNumber.

setLocation(String) - Method in class de.isas.mztab2.model.MsRun

Set location.

setMaxErrorCount(int) - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Define the maximum number of errors recorded by this list before an
 MZTabErrorOverflowException
 is thrown

setMessage(String) - Method in class de.isas.mztab2.model.Error

Set message.

setMessage(String) - Method in class de.isas.mztab2.model.ValidationMessage

Set message.

setMessageType(ValidationMessage.MessageTypeEnum) - Method in class de.isas.mztab2.model.ValidationMessage

Set messageType.

setMetadata(Metadata) - Method in class de.isas.mztab2.model.MzTab

Set metadata.

setMsg(String) - Method in class de.isas.mztab2.model.Comment

Set msg.

setMsLevel(Parameter) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set msLevel.

setMsRun(MsRun) - Method in class de.isas.mztab2.model.SpectraRef

Set msRun.

setMsRun(List<MsRun>) - Method in class de.isas.mztab2.model.Metadata

Set msRun.

setMsRunRef(List<MsRun>) - Method in class de.isas.mztab2.model.Assay

Set msRunRef.

setMzTabID(String) - Method in class de.isas.mztab2.model.Metadata

Set mzTabID.

setMzTabVersion(String) - Method in class de.isas.mztab2.model.Metadata

Set mzTabVersion.

setName(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set name.

setName(String) - Method in class de.isas.mztab2.model.Assay

Set name.

setName(String) - Method in class de.isas.mztab2.model.Contact

Set name.

setName(String) - Method in class de.isas.mztab2.model.MsRun

Set name.

setName(String) - Method in class de.isas.mztab2.model.Parameter

Set name.

setName(String) - Method in class de.isas.mztab2.model.Sample

Set name.

setName(String) - Method in class de.isas.mztab2.model.StudyVariable

Set name.

setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set opt.

setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set opt.

setOpt(List<OptColumnMapping>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set opt.

setParam(Parameter) - Method in class de.isas.mztab2.model.ColumnParameterMapping

Set param.

setParam(Parameter) - Method in class de.isas.mztab2.model.Database

Set param.

setParam(Parameter) - Method in class de.isas.mztab2.model.OptColumnMapping

Set param.

setParameter(Parameter) - Method in class de.isas.mztab2.model.Software

Set parameter.

setPrefix(Comment.PrefixEnum) - Method in class de.isas.mztab2.model.Comment

Set prefix.

setPrefix(Metadata.PrefixEnum) - Method in class de.isas.mztab2.model.Metadata

Set prefix.

setPrefix(String) - Method in class de.isas.mztab2.model.Database

Set prefix.

setPublication(List<Publication>) - Method in class de.isas.mztab2.model.Metadata

Set publication.

setPublicationItems(List<PublicationItem>) - Method in class de.isas.mztab2.model.Publication

Set publicationItems.

setQuantificationMethod(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set quantificationMethod.

setRank(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set rank.

setReference(String) - Method in class de.isas.mztab2.model.SpectraRef

Set reference.

setReliability(String) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set reliability.

setRetentionTimeInSeconds(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSeconds.

setRetentionTimeInSecondsEnd(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSecondsEnd.

setRetentionTimeInSecondsStart(Double) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set retentionTimeInSecondsStart.

setSample(List<Sample>) - Method in class de.isas.mztab2.model.Metadata

Set sample.

setSampleProcessing(List<Parameter>) - Method in class de.isas.mztab2.model.SampleProcessing

Set sampleProcessing.

setSampleProcessing(List<SampleProcessing>) - Method in class de.isas.mztab2.model.Metadata

Set sampleProcessing.

setSampleRef(Sample) - Method in class de.isas.mztab2.model.Assay

Set sampleRef.

setScanPolarity(List<Parameter>) - Method in class de.isas.mztab2.model.MsRun

Set scanPolarity.

setSetting(List<String>) - Method in class de.isas.mztab2.model.Software

Set setting.

setSmallMoleculeEvidence(List<SmallMoleculeEvidence>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeEvidence.

setSmallMoleculeFeature(List<SmallMoleculeFeature>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeFeature.

setSmallMoleculeFeatureQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeFeatureQuantificationUnit.

setSmallMoleculeIdentificationReliability(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeIdentificationReliability.

setSmallMoleculeQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Set smallMoleculeQuantificationUnit.

setSmallMoleculeSummary(List<SmallMoleculeSummary>) - Method in class de.isas.mztab2.model.MzTab

Set smallMoleculeSummary.

setSmeId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set smeId.

setSmeIdRefAmbiguityCode(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smeIdRefAmbiguityCode.

setSmeIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smeIdRefs.

setSmfId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Set smfId.

setSmfIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smfIdRefs.

setSmiles(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set smiles.

setSmiles(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smiles.

setSmlId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set smlId.

setSoftware(List<Software>) - Method in class de.isas.mztab2.model.Metadata

Set software.

setSource(Parameter) - Method in class de.isas.mztab2.model.Instrument

Set source.

setSpecies(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set species.

setSpectraRef(List<SpectraRef>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set spectraRef.

setStudyVariable(List<StudyVariable>) - Method in class de.isas.mztab2.model.Metadata

Set studyVariable.

setTheoreticalMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set theoreticalMassToCharge.

setTheoreticalNeutralMass(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set theoreticalNeutralMass.

setting - de.isas.mztab2.model.Software.Properties
 
setting(List<String>) - Method in class de.isas.mztab2.model.Software

Builder method for setting.

setTissue(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Set tissue.

setTitle(String) - Method in class de.isas.mztab2.model.Metadata

Set title.

setType(PublicationItem.TypeEnum) - Method in class de.isas.mztab2.model.PublicationItem

Set type.

setUri(String) - Method in class de.isas.mztab2.model.CV

Set uri.

setUri(String) - Method in class de.isas.mztab2.model.Database

Set uri.

setUri(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Set uri.

setUri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Set uri.

setUri(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Set uri.

setValue(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Set value.

setValue(String) - Method in class de.isas.mztab2.model.Parameter

Set value.

setValue(String) - Method in class de.isas.mztab2.model.Uri

Set value.

setVariationFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Set variationFunction.

setVersion(String) - Method in class de.isas.mztab2.model.CV

Set version.

setVersion(String) - Method in class de.isas.mztab2.model.Database

Set version.

SFH - de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
 
SingleStudyVariableName - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SingleStudyVariableName

size() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Returns the number of elements in this list.

smallMoleculeEvidence - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeEvidence(List<SmallMoleculeEvidence>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeEvidence.

SmallMoleculeEvidence - Class in de.isas.mztab2.model

The small molecule evidence section is table-based, representing evidence for identifications of small molecules/features, from database search or any other process used to give putative identifications to molecules.

SmallMoleculeEvidence() - Constructor for class de.isas.mztab2.model.SmallMoleculeEvidence
 
SmallMoleculeEvidence.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule evidence table header prefix.

SmallMoleculeEvidence.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule evidence table row prefix.

SmallMoleculeEvidence.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeEvidence.

smallMoleculeFeature - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeFeature(List<SmallMoleculeFeature>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeFeature.

SmallMoleculeFeature - Class in de.isas.mztab2.model

The small molecule feature section is table-based, representing individual MS regions (generally considered to be the elution profile for all isotopomers formed from a single charge state of a molecule), that have been measured/quantified.

SmallMoleculeFeature() - Constructor for class de.isas.mztab2.model.SmallMoleculeFeature
 
SmallMoleculeFeature.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule feature table header prefix.

SmallMoleculeFeature.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule feature table row prefix.

SmallMoleculeFeature.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeFeature.

smallMoleculeFeatureQuantificationUnit - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeFeatureQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeFeatureQuantificationUnit.

smallMoleculeIdentificationReliability - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeIdentificationReliability(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeIdentificationReliability.

smallMoleculeQuantificationUnit - de.isas.mztab2.model.Metadata.Properties
 
smallMoleculeQuantificationUnit(Parameter) - Method in class de.isas.mztab2.model.Metadata

Builder method for smallMoleculeQuantificationUnit.

SmallMoleculeSearchEngineScoreNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SmallMoleculeSearchEngineScoreNotDefined

smallMoleculeSummary - de.isas.mztab2.model.MzTab.Properties
 
smallMoleculeSummary(List<SmallMoleculeSummary>) - Method in class de.isas.mztab2.model.MzTab

Builder method for smallMoleculeSummary.

SmallMoleculeSummary - Class in de.isas.mztab2.model

The small molecule summary section is table-based, represented summarized quantitative information across assays and study variables, grouped by identification in rows.

SmallMoleculeSummary() - Constructor for class de.isas.mztab2.model.SmallMoleculeSummary
 
SmallMoleculeSummary.HeaderPrefixEnum - Enum in de.isas.mztab2.model

The small molecule table header prefix.

SmallMoleculeSummary.PrefixEnum - Enum in de.isas.mztab2.model

The small molecule table row prefix.

SmallMoleculeSummary.Properties - Enum in de.isas.mztab2.model

Property enumeration for SmallMoleculeSummary.

SME - de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
 
smeId - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
smeId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for smeId.

smeIdRefAmbiguityCode - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smeIdRefAmbiguityCode(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smeIdRefAmbiguityCode.

smeIdRefs - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smeIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smeIdRefs.

SMF - de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
 
smfId - de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
smfId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeFeature

Builder method for smfId.

smfIdRefs - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smfIdRefs(List<Integer>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smfIdRefs.

SMH - de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
 
smiles - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
smiles - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smiles(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for smiles.

smiles(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smiles.

SML - de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
 
smlId - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
smlId(Integer) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for smlId.

software - de.isas.mztab2.model.Metadata.Properties
 
software(List<Software>) - Method in class de.isas.mztab2.model.Metadata

Builder method for software.

Software - Class in de.isas.mztab2.model

Software used to analyze the data and obtain the reported results.

Software() - Constructor for class de.isas.mztab2.model.Software
 
Software.Properties - Enum in de.isas.mztab2.model

Property enumeration for Software.

SoftwareVersion - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SoftwareVersion

source - de.isas.mztab2.model.Instrument.Properties
 
source(Parameter) - Method in class de.isas.mztab2.model.Instrument

Builder method for source.

species - de.isas.mztab2.model.Sample.Properties
 
species(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Builder method for species.

Species - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.CrossCheckErrorType

Constant Species

SpectraIdFormatNotSupported - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraIdFormatNotSupported

SpectraIdFormatNotValid - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraIdFormatNotValid

spectraRef - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
spectraRef(List<SpectraRef>) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for spectraRef.

SpectraRef - Class in de.isas.mztab2.model

Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification.

SpectraRef - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant SpectraRef

SpectraRef - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SpectraRef

SpectraRef() - Constructor for class de.isas.mztab2.model.SpectraRef
 
SpectraRef.Properties - Enum in de.isas.mztab2.model

Property enumeration for SpectraRef.

StableColumn - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant StableColumn

StringList - Class in de.isas.mztab2.model

A typed list of strings.

StringList - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant StringList

StringList() - Constructor for class de.isas.mztab2.model.StringList
 
studyVariable - de.isas.mztab2.model.Metadata.Properties
 
studyVariable(List<StudyVariable>) - Method in class de.isas.mztab2.model.Metadata

Builder method for studyVariable.

StudyVariable - Class in de.isas.mztab2.model

Specification of study_variable.

StudyVariable() - Constructor for class de.isas.mztab2.model.StudyVariable
 
StudyVariable.Properties - Enum in de.isas.mztab2.model

Property enumeration for StudyVariable.

StudyVariableNotDefined - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant StudyVariableNotDefined

SubstituteIdentifier - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant SubstituteIdentifier





T

TAB - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant TAB='   '

TAB_STRING - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant TABs=""+'       '

theoreticalMassToCharge - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
theoreticalMassToCharge(Double) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for theoreticalMassToCharge.

theoreticalNeutralMass - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
theoreticalNeutralMass(List<Double>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for theoreticalNeutralMass.

tissue - de.isas.mztab2.model.Sample.Properties
 
tissue(List<Parameter>) - Method in class de.isas.mztab2.model.Sample

Builder method for tissue.

title - de.isas.mztab2.model.Metadata.Properties
 
title(String) - Method in class de.isas.mztab2.model.Metadata

Builder method for title.

toCapital(String) - Static method in class uk.ac.ebi.pride.jmztab2.model.MZTabStringUtils

Translate the string to the first char is upper case, others are lower case.

toString() - Method in enum de.isas.mztab2.model.Assay.Properties
 
toString() - Method in class de.isas.mztab2.model.Assay
 
toString() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
toString() - Method in class de.isas.mztab2.model.ColumnParameterMapping
 
toString() - Method in enum de.isas.mztab2.model.Comment.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.Comment.Properties
 
toString() - Method in class de.isas.mztab2.model.Comment
 
toString() - Method in enum de.isas.mztab2.model.Contact.Properties
 
toString() - Method in class de.isas.mztab2.model.Contact
 
toString() - Method in enum de.isas.mztab2.model.CV.Properties
 
toString() - Method in class de.isas.mztab2.model.CV
 
toString() - Method in enum de.isas.mztab2.model.Database.Properties
 
toString() - Method in class de.isas.mztab2.model.Database
 
toString() - Method in enum de.isas.mztab2.model.Error.Properties
 
toString() - Method in class de.isas.mztab2.model.Error
 
toString() - Method in class de.isas.mztab2.model.IndexedElementImpl
 
toString() - Method in enum de.isas.mztab2.model.Instrument.Properties
 
toString() - Method in class de.isas.mztab2.model.Instrument
 
toString() - Method in enum de.isas.mztab2.model.Metadata.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.Metadata.Properties
 
toString() - Method in class de.isas.mztab2.model.Metadata
 
toString() - Method in enum de.isas.mztab2.model.MsRun.Properties
 
toString() - Method in class de.isas.mztab2.model.MsRun
 
toString() - Method in enum de.isas.mztab2.model.MzTab.Properties
 
toString() - Method in class de.isas.mztab2.model.MzTab
 
toString() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
toString() - Method in class de.isas.mztab2.model.OptColumnMapping
 
toString() - Method in enum de.isas.mztab2.model.Parameter.Properties
 
toString() - Method in class de.isas.mztab2.model.Parameter
 
toString() - Method in enum de.isas.mztab2.model.Publication.Properties
 
toString() - Method in class de.isas.mztab2.model.Publication
 
toString() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
 
toString() - Method in class de.isas.mztab2.model.PublicationItem
 
toString() - Method in enum de.isas.mztab2.model.PublicationItem.TypeEnum
 
toString() - Method in enum de.isas.mztab2.model.Sample.Properties
 
toString() - Method in class de.isas.mztab2.model.Sample
 
toString() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
toString() - Method in class de.isas.mztab2.model.SampleProcessing
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeEvidence
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeFeature
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum
 
toString() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
toString() - Method in class de.isas.mztab2.model.SmallMoleculeSummary
 
toString() - Method in enum de.isas.mztab2.model.Software.Properties
 
toString() - Method in class de.isas.mztab2.model.Software
 
toString() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
 
toString() - Method in class de.isas.mztab2.model.SpectraRef
 
toString() - Method in class de.isas.mztab2.model.StringList
 
toString() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
 
toString() - Method in class de.isas.mztab2.model.StudyVariable
 
toString() - Method in enum de.isas.mztab2.model.Uri.Properties
 
toString() - Method in class de.isas.mztab2.model.Uri
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
 
toString() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
toString() - Method in class de.isas.mztab2.model.ValidationMessage
 
toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError



 Code: Unique number for error/warn Category: Currently, there are three
 types of messages: Format, Logical Original: Message expression pattern.
 "{?}"

toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorList

Print error list to string.

toString() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType

Code: Unique number for error/warn
 Category: Currently, there are three types of messages: Format, Logical
 Original: Message expression pattern. "{?}"

toUpper() - Method in enum de.isas.mztab2.model.Assay.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Comment.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Contact.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.CV.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Database.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Error.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Instrument.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Metadata.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.MsRun.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.MzTab.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.OptColumnMapping.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Parameter.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Publication.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.PublicationItem.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Sample.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SampleProcessing.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Software.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.SpectraRef.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.StudyVariable.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.Uri.Properties
 
toUpper() - Method in enum de.isas.mztab2.model.ValidationMessage.Properties
 
toValidationMessage() - Method in class uk.ac.ebi.pride.jmztab2.utils.errors.MZTabError
 
type - de.isas.mztab2.model.PublicationItem.Properties
 
type(PublicationItem.TypeEnum) - Method in class de.isas.mztab2.model.PublicationItem

Builder method for type.





U

uk.ac.ebi.pride.jmztab2 - package uk.ac.ebi.pride.jmztab2

This package contains jmzTab-M model and utility classes that were adapted from the original jmzTab implementation.

uk.ac.ebi.pride.jmztab2.model - package uk.ac.ebi.pride.jmztab2.model

This package contains classes for mzTab-related constants and string utilities.

uk.ac.ebi.pride.jmztab2.utils - package uk.ac.ebi.pride.jmztab2.utils

This package contains the property file mapping for mzTab-M's validation messages.

uk.ac.ebi.pride.jmztab2.utils.errors - package uk.ac.ebi.pride.jmztab2.utils.errors

This package contains error type definitions and related classes used during mzTab validation.

UndefinedStudyVariableNameOnceOnly - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant UndefinedStudyVariableNameOnceOnly

UnknownRefId - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant UnknownRefId

uri - de.isas.mztab2.model.CV.Properties
 
uri - de.isas.mztab2.model.Database.Properties
 
uri - de.isas.mztab2.model.Metadata.Properties
 
uri - de.isas.mztab2.model.SmallMoleculeEvidence.Properties
 
uri - de.isas.mztab2.model.SmallMoleculeSummary.Properties
 
uri(String) - Method in class de.isas.mztab2.model.CV

Builder method for uri.

uri(String) - Method in class de.isas.mztab2.model.Database

Builder method for uri.

uri(String) - Method in class de.isas.mztab2.model.SmallMoleculeEvidence

Builder method for uri.

uri(List<Uri>) - Method in class de.isas.mztab2.model.Metadata

Builder method for uri.

uri(List<String>) - Method in class de.isas.mztab2.model.SmallMoleculeSummary

Builder method for uri.

Uri - Class in de.isas.mztab2.model

A URI pointing to the file’s source data (e.g., a MetaboLights records) or an external file with more details about the study design.

Uri() - Constructor for class de.isas.mztab2.model.Uri
 
URI - de.isas.mztab2.model.PublicationItem.TypeEnum
 
URI - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant URI

Uri.Properties - Enum in de.isas.mztab2.model

Property enumeration for Uri.

URL - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.FormatErrorType

Constant URL





V

validate(MzTab) - Method in class de.isas.lipidomics.mztab2.validation.MzTabValidator
 
validate(MzTab, ValidationMessage.MessageTypeEnum, Validator<MzTab>...) - Static method in class de.isas.lipidomics.mztab2.validation.MzTabValidator

Validate the given mzTab object, filtering messages that are of a lower
 level than the given one.

validate(T) - Method in interface de.isas.lipidomics.mztab2.validation.Validator


 validate.

ValidationMessage - Class in de.isas.mztab2.model

ValidationMessage

ValidationMessage() - Constructor for class de.isas.mztab2.model.ValidationMessage
 
ValidationMessage.CategoryEnum - Enum in de.isas.mztab2.model

Gets or Sets category

ValidationMessage.MessageTypeEnum - Enum in de.isas.mztab2.model

Gets or Sets messageType

ValidationMessage.Properties - Enum in de.isas.mztab2.model

Property enumeration for ValidationMessage.

Validator<T> - Interface in de.isas.lipidomics.mztab2.validation


 Validator interface.

value - de.isas.mztab2.model.OptColumnMapping.Properties
 
value - de.isas.mztab2.model.Parameter.Properties
 
value - de.isas.mztab2.model.Uri.Properties
 
value(String) - Method in class de.isas.mztab2.model.OptColumnMapping

Builder method for value.

value(String) - Method in class de.isas.mztab2.model.Parameter

Builder method for value.

value(String) - Method in class de.isas.mztab2.model.Uri

Builder method for value.

valueOf(String) - Static method in enum de.isas.mztab2.model.Assay.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Comment.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Contact.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.CV.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Database.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Error.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Instrument.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Metadata.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.MsRun.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.MzTab.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Parameter.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Publication.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.PublicationItem.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Sample.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Software.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.SpectraRef.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.StudyVariable.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.Uri.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level

Returns the enum constant of this type with the specified name.

values() - Static method in enum de.isas.mztab2.model.Assay.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ColumnParameterMapping.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Comment.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Comment.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Contact.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.CV.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Database.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Error.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Instrument.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Metadata.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Metadata.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.MsRun.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.MzTab.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.OptColumnMapping.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Parameter.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Publication.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.PublicationItem.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.PublicationItem.TypeEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Sample.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SampleProcessing.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeEvidence.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeFeature.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.HeaderPrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.PrefixEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SmallMoleculeSummary.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Software.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.SpectraRef.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.StudyVariable.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.Uri.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.CategoryEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.MessageTypeEnum

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum de.isas.mztab2.model.ValidationMessage.Properties

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Category

Returns an array containing the constants of this enum type, in
the order they are declared.

values() - Static method in enum uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level

Returns an array containing the constants of this enum type, in
the order they are declared.

VariableMod - Static variable in class uk.ac.ebi.pride.jmztab2.utils.errors.LogicalErrorType

Constant VariableMod

variationFunction - de.isas.mztab2.model.StudyVariable.Properties
 
variationFunction(Parameter) - Method in class de.isas.mztab2.model.StudyVariable

Builder method for variationFunction.

version - de.isas.mztab2.model.CV.Properties
 
version - de.isas.mztab2.model.Database.Properties
 
version(String) - Method in class de.isas.mztab2.model.CV

Builder method for version.

version(String) - Method in class de.isas.mztab2.model.Database

Builder method for version.

VERSION_MZTAB_M - Static variable in class uk.ac.ebi.pride.jmztab2.model.MZTabConstants

Constant VERSION="2.0.0-M"





W

Warn - uk.ac.ebi.pride.jmztab2.utils.errors.MZTabErrorType.Level
 
WARN - de.isas.mztab2.model.ValidationMessage.MessageTypeEnum
 

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